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Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace’s and Lydekker’s Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.

The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate. Ancient human genomes uncover historical hard sweeps Hard sweeps were common in ancient West Eurasian populations A historical hard sweep in the MHC-III region Admixture can obscure historical hard sweeps Evolutionary scenarios underlying sweep signal dilution The mutational basis of the Eurasian hard sweeps Discussion Methods

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic 'super-archaic' species-Homo luzonensis and H. floresiensis-were present around the time anatomically modern humans arrived in the region >50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans-a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes, including >200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.

Who are we? Where did we come from? Why are we here? These fundamental questions have been widespread throughout human history, shared across different cultures from distant epochs and geographical locations. The search has been as much a philosophical as an empirical one, capturing the imagination of the philosopher, the theologian, the artist and the scientist alike. Hence, the quest for unveiling our origins is probably as old as humanity itself. From a scientific point of view, which we address in the present article, the question of human origins became deeply intertwined with Charles Darwin's theory of evolution in the late 19th century. This led to the development of scientific fields such as palaeoanthropology, which analyses fossil remains, stone tools and cultural artefacts to piece together our past. Recently, however, the possibility to assess genetic information from thousands of individuals across the world and, more importantly, to obtain DNA from specimens that lived thousands of years in the past (so-called ancient DNA [aDNA] analyses) is rapidly transforming long-held beliefs about our origins. As such, we have never been in a better position to ask what do our genomes have to tell us about where we came from. Ultimately, however, can they tell us who we are?

The tropical archipelago of Wallacea contains thousands of individual islands interspersed between mainland Asia and Near Oceania, and marks the location of a series of ancient oceanic voyages leading to the peopling of Sahul—i.e., the former continent that joined Australia and New Guinea at a time of lowered sea level—by 50,000 years ago. Despite the apparent deep antiquity of human presence in Wallacea, prior population history research in this region has been hampered by patchy archaeological and genetic records and is largely concentrated upon more recent history that follows the arrival of Austronesian seafarers ~3000–4000 years ago (3–4 ka). To shed light on the deeper history of Wallacea and its connections with New Guinea and Australia, we performed phylogeographic analyses on 656 whole mitogenomes from these three regions, including 186 new samples from eight Wallacean islands and three West Papuan populations. Our results point to a surprisingly dynamic population history in Wallacea, marked by two periods of extensive demographic change concentrated around the Last Glacial Maximum ~15 ka and post-Austronesian contact ~3 ka. These changes appear to have greatly diminished genetic signals informative about the original peopling of Sahul, and have important implications for our current understanding of the population history of the region. 1. Introduction 2. Materials and Methods 2.1. Sample Collection and Ethics 2.2. Mitochondrial Sequence Generation 2.3. Combined Wallacea–Sahul Dataset 2.4. Phylogenetic Parameter Estimation 2.5. Using Ancestral Node Dates from Geographically Exclusive Clades to Infer Demographic History 2.6. Migration Model Inference and Testing 2.7. Simulating and Estimating the Timing of Migration Events 3. Results 3.1. Summary of New Mitochondrial Haplogroups from Wallacea and West Papua 3.2. Phylogeographic Analyses 4. Discussion 4.1. Post-LGM Population Expansions and Movements 4.2. Redistribution of Papuan mtDNA Lineages Following Austronesian Contact 4.3. Comparison with Wallacean Archaeological and Linguistic Records 5. Conclusions

The dispersal of anatomically modern human populations out of Africa and across much of the rest of the world around 55 to 50 thousand years before present (ka) is recorded genetically by the multiple hominin groups they met and interbred with along the way, including the Neandertals and Denisovans. The signatures of these introgression events remain preserved in the genomes of modern-day populations, and provide a powerful record of the sequence and timing of these early migrations, with Asia proving a particularly complex area. At least 3 different hominin groups appear to have been involved in Asia, of which only the Denisovans are currently known. Several interbreeding events are inferred to have taken place east of Wallace’s Line, consistent with archaeological evidence of widespread and early hominin presence in the area. However, archaeological and fossil evidence indicates archaic hominins had not spread as far as the Sahul continent (New Guinea, Australia, and Tasmania), where recent genetic evidence remains enigmatic.

Location modeling techniques have been applied to an extremely wide variety of public facilities. However, their application to one of the most ubiquitous public facilities – courts of justice – has been very rare. In this paper, we describe a study promoted by the Ministry of Justice of Portugal to define a proposal for the country's new judiciary map – that is, the spatial organization of the judicial system. The new map aims to promote the efficiency and specialization of the justice system (leading to better and faster court decisions) and to provide a good level of accessibility to courts. We developed two optimization models addressing those goals – a districting model, to determine the borders of new, large judicial districts; and a court location model, to determine the location, type, size, and coverage area of the courts included in each new district. Both models are discrete facility location models and consider hierarchical facilities – generic courts and specialized courts of multiple types. Our study was publicly acknowledged by the Portuguese government as having contributed to the new judiciary map that has since been approved and implemented.

Mesoamerica is a historically and culturally defined geographic area comprising current central and south Mexico, Belize, Guatemala, El Salvador, and border regions of Honduras, western Nicaragua, and northwestern Costa Rica. The permanent settling of Mesoamerica was accompanied by the development of agriculture and pottery manufacturing (2500 BCE–150 CE), which led to the rise of several cultures connected by commerce and farming. Hence, Mesoamericans probably carried an invaluable genetic diversity partly lost during the Spanish conquest and the subsequent colonial period. Mesoamerican ancient DNA (aDNA) research has mainly focused on the study of mitochondrial DNA in the Basin of Mexico and the Yucatán Peninsula and its nearby territories, particularly during the Postclassic period (900–1519 CE). Despite limitations associated with the poor preservation of samples in tropical areas, recent methodological improvements pave the way for a deeper analysis of Mesoamerica. Here, we review how aDNA research has helped discern population dynamics patterns in the pre-Columbian Mesoamerican context, how it supports archaeological, linguistic, and anthropological conclusions, and finally, how it offers new working hypotheses.

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic 'super-archaic' species-Homo luzonensis and H. floresiensis-were present around the time anatomically modern humans arrived in the region50,000 years ago. Intriguingly, contemporary human populations across ISEA carry distinct genomic traces of ancient interbreeding events with Denisovans-a separate hominin lineage that currently lacks a fossil record in ISEA. To query this apparent disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in400 modern human genomes, including200 from ISEA. Our results corroborate widespread Denisovan ancestry in ISEA populations, but fail to detect any substantial super-archaic admixture signals compatible with the endemic fossil record of ISEA. We discuss the implications of our findings for the understanding of hominin history in ISEA, including future research directions that might help to unlock more details about the prehistory of the enigmatic Denisovans.

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic ‘super-archaic’ species – Homo luzonensis and H. floresiensis – were present around the time anatomically modern humans (AMH) arrived in the region >50,000 years ago. Contemporary human populations carry signals consistent with interbreeding events with Denisovans in ISEA – a species that is thought to be more closely related to AMH than the super-archaic endemic ISEA hominins. To query this disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes. Our results corroborate widespread Denisovan ancestry in ISEA populations but fail to detect any super-archaic admixture signals. By highlighting local megafaunal survival east of the Wallace Line as a potential signature of deep, pre-H. sapiens hominin-faunal interaction, we propose that this understudied region may hold the key to unlocking significant chapters in Denisovan prehistory.

We report detailed peptide binding affinities between 438 HLA Class I and Class II proteins and complete proteomes of seven pandemic human viruses, including coronaviruses, influenza viruses and HIV-1. We contrast these affinities with HLA allele frequencies across hundreds of human populations worldwide. Statistical modelling shows that peptide binding affinities classified into four distinct categories depend on the HLA locus but that the type of virus is only a weak predictor, except in the case of HIV-1. Amongst the strong HLA binders (IC50 ≤?50), we uncovered 16 alleles (the top ones being A*02:02, B*15:03 and DRB1*01:02) binding more than 1% of peptides derived from all viruses, 9 (top ones including HLA-A*68:01, B*15:25, C*03:02 and DRB1*07:01) binding all viruses except HIV-1, and 15 (top ones A*02:01 and C*14:02) only binding coronaviruses. The frequencies of strongest and weakest HLA peptide binders differ significantly among populations from different geographic regions, with Indigenous peoples of America showing both higher frequencies of strongest and lower frequencies of weakest binders. As many HLA proteins are strong binders of peptides from distinct viral families, we discuss this result in relation to possible signatures of natural selection on HLA promiscuous alleles due to undetermined past pathogenic infections. Although highly relevant for evolutionary genetics and the development of vaccine therapies, these results should not lead to forget that individual resistance and vulnerability to diseases go beyond the sole HLA allelic affinity and depend on multiple, complex and often unknown biological, environmental and other variables. This article is protected by copyright. All rights reserved. 1 Introduction 2 Material and methods 2.1 Population samples 2.2 HLA alleles and proteins 2.3 Viral proteins 2.3.1 SARS-CoV-1 2.3.2 SARS-CoV-2 2.3.3 MERS-CoV 2.3.4 A/H1N1 2.3.5 A/H3N2 2.3.6 A/H7N9 2.3.7 HIV-1 2.4 HLA peptide-binding affinity predictions 3 Statistical analyses 3.1 HLA strongest and weakest binders of SARS-CoV-2 peptides in populations worldwide 3.2 HLA strongest and weakest binders of peptides derived from the seven viruses 4 Results 4.1 Binding affinities of HLA-A, -B, -C, -DR and -DQ molecules to SARS-CoV-2 4.2 List of strongest and weakest HLA SARS-CoV-2 peptide binders at each HLA locus 4.2.1 HLA-A 4.2.2 HLA-B 4.2.3 HLA-C 4.2.4 HLA-DR 4.2.5 HLA-DQ 4.3 Global frequency distributions of strongest and weakest HLA SARS-CoV-2 peptide binders 4.4 Effects of HLA locus and geographic region on the global frequency distributions of HLA SARS-CoV-2 peptide binders 4.5 Comparison of the HLA peptidebinding patterns observed for the seven different viruses 4.6 Effects of the kind of binding, the HLA locus and the variety of virus on the proportions of bound peptides 5 Discussion 5.1 Binding affinities of HLA proteins to SARS-CoV-2 and comparison to other viruses 5.2 Global distribution of strongest and weakest HLA SARS-CoV-2 peptide binders in human populations 6 Conclusion

Summary The Southern Cone of South America (SCSA) is a key region for investigations about the peopling of the Americas. However, little is known about the eastern sector, the Argentinian Pampas. We analyzed 18 mitochondrial genomes—7 of which are novel—from human skeletal remains from 3 Early to Late Holocene archaeological sites. The Pampas present a distinctive genetic makeup compared to other Middle to Late Holocene pre-Columbian SCSA populations. We also report the earliest individuals carrying SCSA-specific mitochondrial haplogroups D1j and D1g from Early and Middle Holocene, respectively. Using these deep calibration time points in Bayesian phylogenetic reconstructions, we suggest that the first settlers of the Pampas were part of a single and rapid dispersal ∼15,600 years ago. Finally, we propose that present-day genetic differences between the Pampas and the rest of the SCSA are due to founder effects, genetic drift, and a partial population replacement ∼9,000 years ago., Graphical abstract, Highlights • Analysis of 18 ancient human mitochondrial genomes from the Argentinian Pampas. • Genetic makeup of Early-Mid Holocene Pampas distinct from later neighboring peoples. • Earliest individuals carrying region-specific mitochondrial haplogroups D1j and D1g. • First Pampean settlers were part of a single and rapid dispersal ∼15,600 years ago., Genetics; Genomics; Paleogenetics

Selective pressures imposed by pathogens have varied among human populations throughout their evolution, leading to marked inter-population differences at some genes mediating susceptibility to infectious and immune-related diseases. Here, we investigated the evolutionary history of a common polymorphism resulting in a Y529 versus C529 change in the cadherin related family member 3 (CDHR3) receptor which underlies variable susceptibility to rhinovirus-C infection and is associated with severe childhood asthma. The protective variant is the derived allele and is found at high frequency worldwide (69–95%). We detected genome-wide significant signatures of natural selection consistent with a rapid increase of the haplotypes carrying the allele, suggesting that non-neutral processes have acted on this locus across all human populations. However, the allele has not fixed in any population despite multiple lines of evidence suggesting that the mutation predates human migrations out of Africa. Using an approximate Bayesian computation method, we estimate the age of the mutation while explicitly accounting for past demography and positive or frequency-dependent balancing selection. Our analyses indicate a single emergence of the mutation in anatomically modern humans ~150 000 years ago and indicate that balancing selection has maintained the beneficial allele at high equilibrium frequencies worldwide. Apart from the well-known cases of the MHC and ABO genes, this study provides the first evidence that negative frequency-dependent selection plausibly acted on a human disease susceptibility locus, a form of balancing selection compatible with typical transmission dynamics of communicable respiratory viruses that might exploit CDHR3.

As anatomically modern humans (AMH) migrated out of Africa and around the rest of the world, they met and interbred with multiple extinct hominid species. The traces of genetic input from these past interbreeding events, recorded in the genomes of modern populations, have created a powerful record of recent human migrations. The first of these events occurred between Neandertals, and a small group of AMH shortly after they left Africa, somewhere in western Eurasia around 55-50 ka, and left a genomic signal of about 2% Neandertal DNA that was subsequently spread across the rest of the world. In contrast to the Neandertals, the interbreeding events with other extinct hominid groups – such as the Denisovans, the east Eurasian sister group of Neandertals – remain poorly understood, but are potentially far more complex.

Balancing selection maintains advantageous diversity in populations through various mechanisms. Although extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here, we describe the Non-central Deviation (NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test. NCD can be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, and NCD2 has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup, NCD2 shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: ∼0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows (P

Most human polymorphisms are neutral or slightly deleterious, but some genetic variation is advantageous and maintained in populations by balancing selection. Considered a rarity and overlooked for years, balanced polymorphisms have recently received renewed attention with several lines of evidence showing their relevance in human evolution. From theoretical work on its role in adaptation to empirical studies that identify its targets, recent developments have showed that balancing selection is more prevalent than previously thought. Here we review these developments and discuss their implications in our understanding of the influence of balancing selection in human evolution. We also review existing evidence on the biological functions that benefit most from advantageous diversity, and the functional consequences of these variants. Overall, we argue that balancing selection must be considered an important selective force in human evolution.

Selective pressures imposed by pathogens have varied among human populations throughout their evolution, leading to marked inter-population differences at some genes mediating susceptibility to infectious and immune-related diseases. A common polymorphism resulting in a C529 versus T529 change in the Cadherin-Related Family Member 3 (CDHR3) receptor is associated with rhinovirus-C (RV-C) susceptibility and severe childhood asthma. Given the morbidity and mortality associated with RV-C dependent respiratory infections and asthma, we hypothesized that the protective variant has been under selection in the human population. Supporting this idea, a recent cross-species outbreak of RV-C among chimpanzees in Uganda, which carry the ancestral ‘risk’ allele at this position, resulted in a mortality rate of 8.9%. Using publicly available genomic data, we sought to determine the evolutionary history and role of selection acting on this infectious disease susceptibility locus. The protective variant is the derived allele and is found at high frequency worldwide, with the lowest relative frequency in African populations and highest in East Asian populations. There is minimal population structure among haplotypes, and we detect genomic signatures consistent with a rapid increase in frequency of the protective allele across all human populations. However, given strong evidence that the protective allele arose in anatomically modern humans prior to their migrations out of Africa and that the allele has not fixed in any population, the patterns observed here are not consistent with a classical selective sweep. We hypothesize that patterns may indicate frequency-dependent selection worldwide. Irrespective of the mode of selection, our analyses show the derived allele has been subject to selection in recent human evolution.

Balancing selection maintains advantageous diversity in populations through various mechanisms. While extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here we describe theNon-Central Deviation(NCD), a simple yet powerful statistic to detect long-term balancing selection (LTBS) that quantifies how close frequencies are to expectations under LTBS, and provides the basis for a neutrality test.NCDcan be applied to a single locus or genomic data, and can be implemented considering only polymorphisms (NCD1) or also considering fixed differences with respect to an outgroup (NCD2) species. Incorporating fixed differences improves power, andNCD2has higher power to detect LTBS in humans under different frequencies of the balanced allele(s) than other available methods. Applied to genome-wide data from African and European human populations, in both cases using chimpanzee as an outgroup,NCD2shows that, albeit not prevalent, LTBS affects a sizable portion of the genome: about 0.6% of analyzed genomic windows and 0.8% of analyzed positions. Significant windows (p< 0.0001) contain 1.6% of SNPs in the genome, which disproportionally fall within exons and change protein sequence, but are not enriched in putatively regulatory sites. These windows overlap about 8% of the protein-coding genes, and these have larger number of transcripts than expected by chance even after controlling for gene length. Our catalog includes known targets of LTBS but a majority of them (90%) are novel. As expected, immune-related genes are among those with the strongest signatures, although most candidates are involved in other biological functions, suggesting that LTBS potentially influences diverse human phenotypes.

In this paper we report the results of a study on secondary school planning made within the framework of Coimbra's Educational Charter. Coimbra is a medium-sized municipality of 320 km2 and 150000 inhabitants located in the center-littoral region of Portugal. The planning problem addressed in the study consisted of defining the location, type, and size of the schools that should integrate Coimbra's secondary school network in 2015, given, first, the excess of aggregate school capacity that currently characterizes the municipality, and, second, the change in school typology that needs to be implemented as a consequence of a recent reorganization of the Portuguese educational system. This problem was analyzed with a discrete facility-location model and considers decisions both of closing existing schools and of opening new schools. The model is a variant of the well-known p-median model, which aims at maximizing the accessibility of students to schools, with constraints on maximum and minimum capacity occupation that make model solutions lose the single assignment and closest assignment properties. As these are desirable properties in a public-facility planning context, they are enforced with explicit constraints. The results obtained through the model are discussed from the standpoint of the trade-off between school accessibility improvements and school network changes.

This paper describes a study of planning vehicle routes for the collection of urban recyclable waste. The aim is to create collection routes for every day of the month, to be repeated every month, minimizing the operation cost. Two important features of the problem are the planning of a relatively long period of time and the separate collection of three types of waste. The collection operation was modelled in accordance to the practice of the company that manages the collection system. Heuristic techniques were developed to solve the model in three phases: definition of the geographic zones served by the vehicles, definition of the waste type to collect on each day of the month, definition of the collection routes. Preliminary results suggest that significant economies in collection costs are possible.

The majority of genetic studies on Jewish populations have been focused on Ashkenazim, and genetic data from the Sephardic original source, the Iberian Peninsula, are particularly scarce. Regarding the mitochondrial genome, the available information is limited to a single Portuguese village, Belmonte, where just two different lineages (a single one corresponding to 93.3%) were found in 30 individuals. Aiming at disclosing the ancestral maternal background of the Portuguese Jewry, we enlarged the sampling to other crypto-Jewish descendants in the Braganca district (NE Portugal). Fifty-seven complete mtDNA genomes were newly sequenced and — in contrast with Belmonte — a high level of diversity was found, with five haplogroups (HV0b, N1, T2b11, T2e and U2e) being putatively identified as Sephardic founding lineages. Therefore — in sharp contrast with Belmonte — these communities have managed to escape the expected inbreeding effects caused by centuries of religious repression and have kept a significant proportion of the Sephardic founder gene pool. This deeper analysis of the surviving Sephardic maternal lineages allowed a much more comprehensive and detailed perspective on the origins and survival of the Sephardic genetic heritage. In line with previously published results on Sephardic paternal lineages, our findings also show a surprising resistance to the erosion of genetic diversity in the maternal lineages.

Balancing selection maintains advantageous genetic and phenotypic diversity in populations. When selection acts for long evolutionary periods selected polymorphisms may survive species splits and segregate in present-day populations of different species. Here, we investigate the role of long-term balancing selection in the evolution of protein-coding sequences in the Homo-Pan clade. We sequenced the exome of 20 humans, 20 chimpanzees, and 20 bonobos and detected eight coding trans-species polymorphisms (trSNPs) that are shared among the three species and have segregated for approximately 14 My of independent evolution. Although the majority of these trSNPs were found in three genes of the major histocompatibility locus cluster, we also uncovered one coding trSNP (rs12088790) in the gene LAD1. All these trSNPs show clustering of sequences by allele rather than by species and also exhibit other signatures of long-term balancing selection, such as segregating at intermediate frequency and lying in a locus with high genetic diversity. Here, we focus on the trSNP in LAD1, a gene that encodes for Ladinin-1, a collagenous anchoring filament protein of basement membrane that is responsible for maintaining cohesion at the dermal-epidermal junction; the gene is also an autoantigen responsible for linear IgA disease. This trSNP results in a missense change (Leucine257Proline) and, besides altering the protein sequence, is associated with changes in gene expression of LAD1.

We compare three modelling approaches to univariate time series forecasting, based on recursive estimation and supervised learning methods. The models considered range from relatively simple time-varying parameter damped trend models to non-linear models based on radial basis function ‘networks’ or multi-layer perceptrons. The estimation methods considered are the Kalman filter procedure, the Recursive Least Squares algorithm and variants, and the Levenberg-Marquardt algorithm, which we try to describe under a common framework. As our main goals, we discuss some of the main identification and estimation issues associated with those approaches, and illustrate their application through the study of selected data from the Lisbon stock exchange index.

The authors of Nogueiro et al1 do thank Bedford and Yacobi comments on our paper providing the opportunity to clarify some issues that may have been put forward in an insufficiently clear or poorly phrased manner. We must begin by restating the framework in which the paper was worked out; considering that the Iberian Peninsula constitutes the original geographic/historical source of Sephardic populations, the main goal was to characterize complete mitogenomes from self-designated Jews from north-eastern Portugal. The pertinence of the study lays on that the majority of previous studies (Belmonte2 and Mallorca3 excluded) were based in descents from exiled Sephardic communities with a supposed Iberian origin rather than those who stayed in Iberia and constitute the remains of the original Sephardic population. Accordingly, all previous works reporting maternal Sephardic lineages were addressed including those published by Bedford4 and Bedford et al.5 The clades of all haplotypes in Nogueiro et al1 work were assigned according to PhyloTree built 16.6 This nomenclature was adopted during the revision process of the manuscript (see revision track record of Nogueiro et al1 work), since the last version of the PhyloTree was launched on the 19 February 2014. At no moment, we intended to credit to us the authorship of the definition of any new branch of the mitochondrial DNA (mtDNA) phylogenetic tree, as clearly stated in the text. The purpose of the phylogenetic tree of global human mtDNA variation and haplogroup nomenclature (www.phylotree.org) is to provide, as stated by the curators, a framework to the scientific community with update information from novel mitogenomes sequences.6 This tool has greatly improved the way researchers can transmit, compare and contribute with their results to the global mtDNA phylogeny knowledge. In this sense, as far as we understand, when a specific PhyloTree built is cited, it is credited to all contributors, as references of mitogenomes upon which a specific branch is based are always quoted. In consequence, we do not understand the purpose of the Bedford and Yacobi7 letter concerning the credit of authorship attribution of the two Jewish clades. We do think to have followed the standard procedures in this matter but we apologize if, by any means that we have not intended, our text can be interpreted as implying an inappropriate authorship attribution. Regarding the first specific branch addressed in Bedford and Yacobi,7 T2e1b (and T2e1b1), as referred in Nogueiro et al,1 was newly included in the PhyloTree build 16 (van Oven and Kayser6) based on three quoted mitogenomes (GenBank accession numbers: {"type":"entrez-nucleotide","attrs":{"text":"KF048033","term_id":"505490414"}}KF048033, {"type":"entrez-nucleotide","attrs":{"text":"KF577586","term_id":"545719589"}}KF577586 and {"type":"entrez-nucleotide","attrs":{"text":"EF556188","term_id":"145967989"}}EF556188). In fact, Bedford et al5 submitted two of these mitogenomes, the remaining one being contributed by Behar et al.2 Although the claims contained in Bedford and Yacobi7 could start a more transversal debate, we consider that in this specific issue no further acknowledgment should be expected as branches of the mitochondrial phylogenetic tree are not sponsored/personal domains. Otherwise, the detailed history of any (sub)haplogroup definition would have to be at least summarised, which in fact, for the one under discussion would require a lengthy and tedious description beginning with Torroni et al8 and including all the works having contributed for the definition of the branch. Concerning the complete mitogenomes used to construct the most parsimonious tree of the analysed clades in Nogueiro et al1 (Supplementary Figures 2), all the information regarding accession numbers (GenBank and EMPOP), sample IDs (mDNA community) and/or direct citations is included. For example, following the corresponding links of any accession number, the information publicly available at GenBank includes: Authors, Title, Journal, Location and Ethnicity, among other details. Whenever ambiguous information was found, we have contacted by email the respective authors for clarification as it happened indeed with Felice L. Belford among others. This added information was duly mentioned in the Acknowledgments section. Furthermore, in no part of the work of Nogueiro et al,1 the ethnicity of the samples used for comparisons is credited to us. Again, Bedford and Yacobi7 comments concerning this topic could lead to an interesting discussion focused on the presence of shared female lineages between Bedford4 and Bedford et al5 previous works and the Portuguese Jews. Considering now T2e1a1a, as for T2e1b, a new branch in the PhyloTree build 16 (van Oven and Kayser6) was included. This branch was defined based on a mitogenome (GenBank accession number: {"type":"entrez-nucleotide","attrs":{"text":"KF657641","term_id":"545719505"}}KF657641) from Bedford et al5 as can be observed in PhyloTree build 16 search. This is a sample from Mexico: Nuevo Leon and together with three other samples from Bedford et al4, 5 ({"type":"entrez-nucleotide","attrs":{"text":"KF577587","term_id":"545719533"}}KF577587, {"type":"entrez-nucleotide","attrs":{"text":"KF577589","term_id":"545719519"}}KF577589 and {"type":"entrez-nucleotide","attrs":{"text":"JN819272","term_id":"356995982"}}JN819272) establish a clade where the Portuguese Sephardic Jews are included (T2e1a1a1) in Nogueiro et al1 (Supplementary Figure 6). With the exception of {"type":"entrez-nucleotide","attrs":{"text":"JN819272","term_id":"356995982"}}JN819272, a Sephardic Jew from Salonica, the other two samples are from Mexico, Tamaulipas and from Texas, USA and could have an eventual Iberian/Sephardic origin. The fact that we have observed two Jewish Sephardic sequences in the NE Portugal sharing the same motif described by Bedford et al,4, 5 plus two further distinct variants, m.13135G4A and m.7133C4T not previously described, can help to clarify if the putative Iberian origin of the Mexican/USA samples is indeed owing to Sephardic ancestry. It is remarkable that T2e1b and U2e1a clades include mitogenomes from both Sephardic and Ashkenazi origins. We do recognise that Bedford et al5 have suggested the two possible scenarios for the T2e1b clade that we also consider, either the defining variants for each branch could have arisen before the separation between the two Jewish groups, or there may have been recent admixture between them. However, in Nogueiro et al1 it is stated that: ‘More complete sampling and complete sequences will contribute to the clarification of which one is more likely. In any case, it must be said that although not frequent, marriages between the two communities occurred (especially) in the sixteenth and seventeenth centuries, namely among the elite sugar traders, with the descendants assimilated into the Ashkenazi community.'9, 10 Thus, specific historical documents regarding the community here analysed were brought to shed light on this specific question providing new evidence to reconstruct a more detailed and accurate history of the Sephardic Jews. Finally, Bedford and Yacobi raise a very interesting question based on the large excess of nonsynonymous over synonymous mutations. This has been detected previously in mtDNA phylogeny (younger mutations are enriched in the first type, so that they often define branch tips) and a lot of debate on the selective pressures acting upon is ongoing11, 12, 13, 14, 15, 16 (and was also detected in animal models as our group has shown in lab mouse17). The issue is, however, extraneous to the topic and goals of our paper; we can nevertheless clarify, as requested, that the finding does not result from a ‘special clinical population of subjects'. We certainly do agree that to know ‘whether this is a coincidence, [or] a notable finding […] would be helpful for evaluating the representativeness of […] [our] results for Sephardim in Northeast Portugal and elsewhere'. Unfortunately, the answer to this alternative requires a much larger sampling effort and the cooperation of the scientific community devoted to demographic history of human maternal lineages as revealed by mtDNA.

In this article, we present a discrete hierarchical location model for public facility planning. The main features of the model are: an accessibility maximization objective; several levels of demand and of facilities; a nested hierarchy of facilities (i.e. a facility of a given level can serve demand of equal and lower levels); maximum and minimum capacity constraints; and user-to-facility assignment constraints. The latter include single-assignment and closest-assignment constraints, as well as a new type of constraints called path-assignment constraints. Their purpose is to enforce some desirable properties for the spatial pattern of assignments. If they are not included, model solutions are difficult to interpret and to explain in a public facility planning context, therefore being less likely to be accepted by the users. The usefulness of the model is illustrated through a real-world application to school network planning. http://www.sciencedirect.com/science/article/B6VCT-4MTK958-1/1/9fe9b0b4466da79a4b6772795371e489

The cultural phenomenon of Crypto-Judaism, defined as the secret adherence to Judaism while publicly professing another faith, arose in Portugal in the beginning of the 16th century after the Decree of Expulsion and the establishment of the Inquisition. Surprisingly, the scientific community acknowledged the persistence of Crypto-Judaic communities at the beginning of the 20th century in central and north-eastern regions of the country (e.g. Braganca). In the present work, we have sampled 56 unrelated individuals from the Braganca Jewish community aiming to characterize their maternal lineage. A 3348bp mtDNA fragment was amplified and sequenced using mitochondrial-specific primers in order to obtain the entire control region. Haplogroup classification was performed according to current nomenclature. High frequencies were found for haplogroups H, HV0, T2, U2 and N1, indicating some degree of European admixture along with a remarkable signature of a Near East ancestry. These data confirm that the Crypto-Jews from Braganca were able to maintain not only their cultural identity but also some ancestral genetic identity, showing a significant population substructure within Portugal, with forensic relevance.